Coffee can contain small amounts of toxins like pesticide residues, mycotoxins, acrylamide, PAHs, and phthalates. Levels are typically very low, but it’s still a good idea to minimize your toxic load by choosing brands that use third-party-testing and publish their results.
America’s favorite morning beverage offers impressive wellness benefits, including healthier aging and protection from heart disease. But are you also consuming chemicals that could harm your health each day?
Here’s what to know about:
- Toxins in coffee
- How concerned you should be
- Third-party-tested brands to help you brew a cleaner, healthier cup
Common toxins in coffee
Coffee can contain certain toxins that, in large amounts, may contribute to health problems. Here are some of the most common offenders.
1. Pesticide and herbicide residue
Like most crops, coffee is vulnerable to pests and weeds. As a result, farmers often treat coffee plants with pesticides and herbicides. Unfortunately, residues of these chemicals may still be present on the beans you brew each morning.
One particularly concerning type is organophosphorus pesticides (OPPs). Studies show that OPPs block acetylcholinesterase, an essential enzyme for nervous system function.
Long-term exposure can lead to:
- Muscle damage
- Depression and other mental health issues
- Cognitive decline
- Higher risks of Parkinson’s disease
- Certain cancers
Researchers believe these effects are due to an increase in oxidative stress and mitochondrial damage.
Another chemical found on coffee beans is aminomethylphosphonic acid (AMPA). AMPA is a breakdown product of glyphosate, the controversial herbicide linked to:
- Cancer
- Liver inflammation
- Metabolic syndrome
Glyphosate is banned in organic farming. However, a study conducted by the Clean Label Project found AMPA in 100% of organic coffee samples tested, with levels averaging 5% higher than in conventional brands.
“Consumers assume that labels like ‘organic’ mean protection from chemicals like glyphosate, but our data shows that’s not always the case,” says Clean Label Project’s Executive Director, Molly Hamilton.
“The detection of AMPA in 100% of organic samples is a wake-up call,” she adds. “Whether from environmental runoff or legacy contamination, this finding highlights the need for stronger safeguards and greater transparency in our food system.”
To lower your exposure, look for brands that test for pesticide residues–not just the organic label.
2. Mycotoxins
Mycotoxins are potentially harmful compounds produced by molds that can grow on coffee beans–especially when stored in warm, humid conditions. The two most common types in coffee are aflatoxin B1 and ochratoxin A.
Aflatoxin B1 is classified as a carcinogen, and ochratoxin A as a possible carcinogen by the International Agency for Research on Cancer (IARC), which is a part of the World Health Organization.
These compounds are extremely prevalent. According to several studies, you’ll find them in:
- 33% of green coffee beans from Brazil
- 18% of brewed coffee samples in Portugal
- 27% of roasted coffees, with the highest aflatoxin levels in decaf
Instant and decaffeinated coffee tend to contain more mycotoxins. But even then, levels are typically below international safety limits.
That said, these compounds also show up in other common foods, such as:
- Grains
- Nuts
- Spices
- Dried fruits
So coffee may be adding to your cumulative exposure.
The good news is that roasting can reduce mycotoxin levels by up to 96%. Storing beans properly after harvesting also helps prevent contamination from happening in the first place.
To be safe, choose high-quality coffee brands that test for mycotoxins, and always store your beans in a cool, dry, airtight container.
3. Roasting byproducts (Acrylamide, PAHs)
Roasting coffee gives it flavor, but it also creates chemical byproducts with potential health risks. The most well-known is acrylamide, which the IARC classifies as a probable human carcinogen.
Animal studies have also linked this chemical to:
- Nerve damage
- Possible reproductive harm
- Gastrointestinal damage
While research in humans is ongoing, it still may be worth watching your acrylamide intake–especially if you drink coffee every day.
Acrylamide forms early in the roasting process and breaks down with extended heat exposure. So, light roasts contain the most, while darker roasts generally have less.
Instant coffee may contain higher levels as well, since the brewing and dehydration process can cause acrylamide to become concentrated.
Another common group of toxins is polycyclic aromatic hydrocarbons (PAHs), which also form at high temperatures. While levels in coffee are typically very low, some PAHs are known carcinogens and could lead to neurotoxicity.
Other heat-related byproducts include:
- Furan, a volatile compound formed in heat-treated foods
- 4-methylimidazole: a byproduct of the Maillard reaction, the natural browning process that happens when heat transforms sugars and proteins
Both of these chemicals can lead to liver damage and higher risks of cancer, according to animal studies.
Again, coffee typically contains very small amounts of these toxins. But it’s smart to reduce your exposure by opting for high-quality, third-party-tested beans from brands that value transparency.
4. Phthalates
Phthalates are chemicals used to make plastics flexible. They’re extremely common in:
- Food packaging
- Cosmetics
- Cleaning products
But they’re also endocrine disruptors–chemicals that interfere with hormones. In fact, numerous studies have linked phthalates to:
- Reproductive problems
- Immune dysfunction
- Asthma and allergies
- Obesity
Phthalates can leach into coffee from:
- Packaging (cans, pods, plastic-lined bags)
- Processing equipment
- Even your coffee maker or other brewing device
Unfortunately, they can also enter the food chain through contaminated water and soil.
The Clean Label Project found higher phthalate levels in canned and pod coffee than bagged varieties. This suggests that packaging is a major source of contamination when it comes to coffee.
To lower your exposure, look for coffee sold in non-plastic containers, and use a plastic-free brewing device whenever possible.
Non-toxic coffee brands
Again, just because a coffee is labeled USDA Organic doesn’t guarantee it’s free of contaminants.
Here are some safer coffees to consider, as identified by the Clean Label Project and other independent testers:
- 365 Organic Caramel Medium Roast
- Starbucks Colombia Medium Roast Pods
- Dunkin Donuts Hazelnut Medium Roast
- Eight O’Clock Original Roast
- Fabula Organic Dark Roast Pods
- Groundwork’s Organic Ethiopia
- Illy’s Classico Medium Roast
- Kicking Horse Three Sisters Medium
- Nespresso Diavolitto Dark Roast Pods
- Newman’s Own Organic Special Blend Pods
- Peace Coffee Organic Birchwood Medium Roast Bag
- Holistic Roasters BioDynamic Organic Medium or Dark Roasts
- Peak Performance Medium or Dark Roast
As always, it’s smart to do your own research. Check each brand’s website for third-party testing information, certifications, and transparency around sourcing and processing to find the best non-toxic and mold-free coffee for you.
Final thoughts on chemicals in coffee
Your morning coffee is a complex mix of natural, healthy compounds–and, potentially, harmful contaminants.
While coffee beans usually contain only trace amounts of toxins, minimizing your exposure to substances like OPPs, AMPA, mycotoxins, acrylamide, and phthalates can help reduce your overall toxic load.
You can do this by choosing high-quality, carefully processed coffee from brands that test for toxins and publish their results; as well as controlling how much you drink.
With a little awareness, you can enjoy your favorite brew with more confidence, knowing that you’re supporting your well-being over the long haul.
References:
A review on the pesticides in coffee: Usage, health effects, detection, and mitigation – PMC
GC-MS/MS and LC-MS/MS analysis followed by risk ranking of mepiquat and pyrethroids in coffee – ScienceDirect
Mycotoxins | FDA
Mycotoxins’ Toxicological Mechanisms Involving Humans, Livestock and Their Associated Health Concerns: A Review – PMC
Ochratoxin A: A Possible Carcinogen
National Coffee Data Trends 2025
Impact of Coffee Consumption on Cardiovascular Health – PMC
Neurotoxic Effects of Pesticides: Implications for Neurodegenerative and Neurobehavioral Disorders – PMC
Lysosomal genes contribute to Parkinson’s disease near agriculture with high intensity pesticide use
Contamination levels of organophosphorus and synthetic pyrethroid pesticides in cocoa beans from Ghana – ScienceDirect
Organophosphate Toxicity – StatPearls – NCBI Bookshelf.
Full article: Occurrence, importance and control of mycotoxins: A review
Ochratoxin A and human health risk: A review of the evidence – PMC
Ochratoxin A in coffee beans (Coffea arabica L.) processed by dry and wet methods – ScienceDirect
Occurrence of ochratoxin A in roasted coffee samples commercialized in Portugal – ScienceDirect
Mechanisms of Neurotoxicity of Organophosphate Pesticides and Their Relation to Neurological Disorders – PMC
Prevalence of toxigenic fungi and mycotoxins in Arabic coffee (Coffea arabica): Protective role of traditional coffee roasting, brewing and bacterial volatiles
Comparison of clean-up methods for ochratoxin A on wine, beer, roasted coffee and chili commercialized in Italy – PubMed
Insights into acrylamide and furanic compounds in coffee with a focus on roasting methods and additives – ScienceDirect
Factors Affecting the Formation of Acrylamide in Coffee
Acrylamide and Cancer Risk
Association of diet with per- and polyfluoroalkyl substances in plasma and human milk in the New Hampshire Birth Cohort Study – ScienceDirect
Determination of polycyclic aromatic hydrocarbons in roasted coffee – PMC.
Insights into acrylamide and furanic compounds in coffee with a focus on roasting methods and additives – PubMed
Coffee Study – Clean Label Project
Aminomethylphosphonic Acid (AMPA), a Glyphosate Metabolite, Decreases Plasma Cholinesterase Activity in Rats – PMC
Coffee growing altitude influences the microbiota, chemical compounds and the quality of fermented coffees – ScienceDirect
The generation of coffee flavor compounds from fresh cherry to cup: deciphering the contribution of microbiota metabolism – ScienceDirect
From Plantation to Cup: Changes in Bioactive Compounds during Coffee Processing – PMC
Thermal Contaminants in Coffee Induced by Roasting: A Review – PMC
Physiology, Acetylcholinesterase – PubMed
Pilot study on the urinary excretion of the glyphosate metabolite aminomethylphosphonic acid and breast cancer risk: The Multiethnic Cohort study – ScienceDirect
Occurrence of Phthalate Esters in Coffee and Risk Assessment – PMC
Effects of Long-Term Exposure to Organophosphate Pesticides in Humans – Gulf War and Health
Phthalates and Their Impacts on Human Health – PMC
